Check results for 'Rcell'

using R version 2.15.0 (2012-03-30)
using platform: i386-apple-darwin9.8.0 (32-bit)
using session charset: ASCII
checking for file 'Rcell/DESCRIPTION' ... OK
checking extension type ... Package
this is package 'Rcell' version '1.1-8'
package encoding: latin1
checking package namespace information ... OK
checking package dependencies ... NOTE
Packages suggested but not available for checking:
'hopach' 'EBImage'
checking if this is a source package ... OK
checking if there is a namespace ... OK
checking for executable files ... OK
checking whether package 'Rcell' can be installed ... OK
checking installed package size ... OK
checking package directory ... OK
checking for portable file names ... OK
checking for sufficient/correct file permissions ... OK
checking DESCRIPTION meta-information ... OK
checking top-level files ... OK
checking index information ... OK
checking package subdirectories ... OK
checking R files for non-ASCII characters ... OK
checking R files for syntax errors ... OK
checking whether the package can be loaded ... OK
checking whether the package can be loaded with stated dependencies ... OK
checking whether the package can be unloaded cleanly ... OK
checking whether the namespace can be loaded with stated dependencies ... OK
checking whether the namespace can be unloaded cleanly ... OK
checking for unstated dependencies in R code ... OK
checking S3 generic/method consistency ... OK
checking replacement functions ... OK
checking foreign function calls ... OK
checking R code for possible problems ... NOTE
.axis: no visible global function definition for 'Image'
.axis: no visible binding for global variable 'img_coord'
.axis: no visible binding for global variable 'pos'
.axis: no visible binding for global variable 'cellID'
.axis: no visible global function definition for 'drawtext'
.axis: no visible global function definition for 'drawfont'
.axis: no visible global function definition for 'rotate'
.grid: no visible binding for global variable 'factor_id_x'
.grid: no visible binding for global variable 'factor_id_y'
.grid: no visible binding for global variable 'factor_id'
.grid: no visible binding for global variable 'factor_x'
.grid: no visible binding for global variable 'factor_y'
.restructure.split.image: no visible binding for global variable
'cellID'
.restructure.split.image: no visible binding for global variable
'posfix'
.restructure.split.image: no visible binding for global variable 'name'
.sample.N.ucid: no visible binding for global variable 'ucid'
.wrap: no visible binding for global variable 'factor_id'
QC.execute: no visible binding for global variable 'QC'
[.cell.data: no visible binding for global variable 'QC'
append.anular.c: no visible binding for global variable 'f.tot.p1.c'
append.anular.c: no visible binding for global variable 'f.tot.c'
append.anular.c: no visible binding for global variable 'f.tot.m1.c'
append.anular.c: no visible binding for global variable 'f.tot.m2.c'
append.anular.c: no visible binding for global variable 'f.tot.m3.c'
append.anular.c: no visible binding for global variable 'a.tot.p1'
append.anular.c: no visible binding for global variable 'a.tot'
append.anular.c: no visible binding for global variable 'a.tot.m1'
append.anular.c: no visible binding for global variable 'a.tot.m2'
append.anular.c: no visible binding for global variable 'a.tot.m3'
append.anular.r: no visible binding for global variable 'f.tot.p1.r'
append.anular.r: no visible binding for global variable 'f.tot.r'
append.anular.r: no visible binding for global variable 'f.tot.m1.r'
append.anular.r: no visible binding for global variable 'f.tot.m2.r'
append.anular.r: no visible binding for global variable 'f.tot.m3.r'
append.anular.r: no visible binding for global variable 'a.tot.p1'
append.anular.r: no visible binding for global variable 'a.tot'
append.anular.r: no visible binding for global variable 'a.tot.m1'
append.anular.r: no visible binding for global variable 'a.tot.m2'
append.anular.r: no visible binding for global variable 'a.tot.m3'
append.anular.y: no visible binding for global variable 'f.tot.p1.y'
append.anular.y: no visible binding for global variable 'f.tot.y'
append.anular.y: no visible binding for global variable 'f.tot.m1.y'
append.anular.y: no visible binding for global variable 'f.tot.m2.y'
append.anular.y: no visible binding for global variable 'f.tot.m3.y'
append.anular.y: no visible binding for global variable 'a.tot.p1'
append.anular.y: no visible binding for global variable 'a.tot'
append.anular.y: no visible binding for global variable 'a.tot.m1'
append.anular.y: no visible binding for global variable 'a.tot.m2'
append.anular.y: no visible binding for global variable 'a.tot.m3'
append.in.focus: no visible binding for global variable 'pos'
append.in.focus: no visible binding for global variable 'z.scan'
append.memRec.y: no visible binding for global variable 'f.tot.m3.y'
append.memRec.y: no visible binding for global variable 'a.tot.m3'
append.memRec.y: no visible binding for global variable 'f.local.bg.y'
append.memRec.y: no visible binding for global variable 'maj.axis'
append.memRec.y: no visible binding for global variable 'min.axis'
append.memRec.y: no visible binding for global variable 'f.m2.y'
append.memRec.y: no visible binding for global variable 'a.m2'
append.memRec.y: no visible binding for global variable 'f.m1.y'
append.memRec.y: no visible binding for global variable 'a.m1'
append.memRec.y: no visible binding for global variable 'f.m0.y'
append.memRec.y: no visible binding for global variable 'a.m0'
append.memRec.y: no visible binding for global variable 'f.p1.y'
append.memRec.y: no visible binding for global variable 'a.p1'
append.memRec.y: no visible binding for global variable 'f.mem.y'
append.memRec.y: no visible binding for global variable 'f.int.y'
append.oif.interval: no visible binding for global variable 'pos'
append.oif.time: warning in chron(times = substring(oif[oif.s + 1, ],
32, 40), format = c("h:m:s")): partial argument match of 'times' to
'times.'
append.oif.time: no visible binding for global variable 'pos'
append.oif.time: no visible binding for global variable 'oif.hour'
append.oif.time: no visible binding for global variable 'oif.msec'
append.oif.time: no visible binding for global variable 'D.oif.hour'
append.oif.time: no visible binding for global variable 'D.oif.msec'
append.oif.time: no visible binding for global variable 'oif.time.s'
append.z.scan: no visible binding for global variable 'pos'
append.z.scan : <anonymous>: no visible binding for global variable
'time.index'
append.z.scan: no visible binding for global variable 't.frame'
append.z.scan: no visible binding for global variable 'time.index'
append.z.scan: no visible binding for global variable 'z.scan'
append.z.scan: no visible binding for global variable 'z.slice'
append.z.scan: no visible binding for global variable 'oif'
as.cell.data.default: no visible binding for global variable 'fluor'
as.cell.data.default: no visible binding for global variable 'bright'
as.cell.data.list: no visible binding for global variable 'fluor'
as.cell.data.list: no visible binding for global variable 'bright'
calc.dist.matrix: no visible binding for global variable 'QC'
cell.hclust: no visible global function definition for 'distancematrix'
cell.hclust: no visible binding for global variable 'subtree'
cell.hclust: no visible binding for global variable 'subtree.n.cell'
chclust: no visible global function definition for 'distancematrix'
chclust: no visible binding for global variable 'subtree'
chclust: no visible binding for global variable 'subtree.n.cell'
cimage.cell.image: no visible global function definition for 'tile'
cimage.cell.image: no visible global function definition for
'normalize'
cimage.cell.image: no visible binding for global variable 'facet_id'
cimage.cell.image : <anonymous>: no visible global function definition
for 'Image'
cimage.cell.image: no visible global function definition for 'Image'
cimage.cell.image: no visible global function definition for 'drawtext'
cimage.cell.image: no visible global function definition for 'drawfont'
cimage.cell.image: no visible binding for global variable 'facet_x'
cimage.cell.image: no visible binding for global variable 'facet_y'
creshape: no visible binding for global variable 'QC'
drawCross: no visible binding for global variable 'Color'
drawLine: no visible binding for global variable 'Color'
fortify.Image: no visible global function definition for 'channel'
get.cell.image.cell.data: no visible binding for global variable 'QC'
get.cell.image.data.frame: no visible binding for global variable
'path.image'
get.cell.image.data.frame: no visible global function definition for
'readImage'
img.desc: no visible global function definition for 'is.Image'
load.cell.data: warning in read.table(fname, sep = "\t", head = TRUE,
colClasses = "numeric"): partial argument match of 'head' to 'header'
load.cell.data: warning in read.table(fname2, sep = "\t", head = TRUE,
as.is = TRUE): partial argument match of 'head' to 'header'
load.cell.data: no visible binding for global variable 'cellID'
load.cell.data: no visible binding for global variable 'pos'
load.cell.data: no visible binding for global variable 'flag'
load.cell.data: no visible binding for global variable 'fluor'
load.cell.data: no visible binding for global variable 'bright'
load.cell.data: no visible binding for global variable 'channel'
load.cellID.data: warning in read.table(fname, sep = "\t", head = TRUE,
colClasses = "numeric"): partial argument match of 'head' to 'header'
load.cellID.data: warning in read.table(fname2, sep = "\t", head =
TRUE, as.is = TRUE): partial argument match of 'head' to 'header'
load.cellID.data: no visible binding for global variable 'cellID'
load.cellID.data: no visible binding for global variable 'pos'
load.cellID.data: no visible binding for global variable 'flag'
load.cellID.data: no visible binding for global variable 'fluor'
load.cellID.data: no visible binding for global variable 'bright'
load.cellID.data: no visible binding for global variable 'channel'
load.pdata: warning in read.table(file = paste(path, "/", pdata, sep =
""), head = TRUE): partial argument match of 'head' to 'header'
print.summary.cell.data: no visible binding for global variable 'undo'
print.summary.cell.data: no visible binding for global variable 'type'
print.summary.cell.data: no visible binding for global variable 'cer'
print.summary.cell.data: no visible binding for global variable
'can.undo'
print.summary.cell.data: no visible binding for global variable
'exclude.vars'
reshape.cell.data: no visible binding for global variable 'QC'
select.cells: no visible binding for global variable 'QC'
show.image: no visible binding for global variable 'QC'
show.image: no visible binding for global variable 'cellID'
show.image: no visible binding for global variable 'xpos'
show.image: no visible binding for global variable 'ypos'
show.img: no visible binding for global variable 'QC'
show.img: no visible binding for global variable 'cellID'
show.img: no visible binding for global variable 'xpos'
show.img: no visible binding for global variable 'ypos'
subset.cell.data: no visible binding for global variable 'QC'
summary.cell.data: no visible binding for global variable '.id'
transform.by.cell.data: no visible binding for global variable 'QC'
update.n.tot: no visible binding for global variable 'ucid'
with.cell.data: no visible binding for global variable 'QC'
checking Rd files ... OK
checking Rd metadata ... OK
checking Rd cross-references ... OK
checking for missing documentation entries ... OK
checking for code/documentation mismatches ... OK
checking Rd \usage sections ... NOTE
S3 methods shown with full name in documentation object 'transform':
'transform.by'

S3 methods shown with full name in documentation object 'update.n.tot':
'update.n.tot'

The \usage entries for S3 methods should use the \method markup and not
their full name.
See the chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
checking Rd contents ... OK
checking for unstated dependencies in examples ... OK
checking contents of 'data' directory ... OK
checking data for non-ASCII characters ... OK
checking data for ASCII and uncompressed saves ... OK
checking sizes of PDF files under 'inst/doc' ... OK
checking installed files from 'inst/doc' ... OK
checking examples ... WARNING
checking a package with encoding 'latin1' in an ASCII locale

OK
checking for unstated dependencies in vignettes ... OK
checking package vignettes in 'inst/doc' ... OK
checking running R code from vignettes ... OK
checking re-building of vignettes ... SKIPPED
checking PDF version of manual ... OK
WARNING: There was 1 warning.
NOTE: There were 3 notes.
See
'/Volumes/Tiger/Builds/Rdev-web/QA/Simon/packages/leopard-universal/results/2.15/Rcell.Rcheck/00check.log'
for details.
elapsed time (check, wall clock): 1:49